Lakes are important sources of greenhouse gases (GHGs), but the drivers of CO2 and CH4 emissions in the aquatic-terrestrial transition zone (ATTZ) of boreal lakes remain poorly understood. This study investigates CO2 and CH4 fluxes in the flooding (A), transition (B), and dry areas (C) of a boreal lake ATTZ. The results showed that CO2 fluxes peaked in the lake ATTZ during summer (85.27 +/- 3.42 mg m(-2) h(-1)). Area C was identified as the primary CO2 emission hotspot, though seasonal variations reversed this trend (A > B > C during autumn). CO2 emissions were primarily driven by CH4 oxidation and organic matter mineralization in area C, while decomposition of organic carbon and microbial respiration were the main contributors in area A. Meanwhile, CH4 fluxes averaged 2.40, 0.49, and 0.35 mg m(-2) h(-1) during summer, spring, and autumn, respectively, with area A exhibiting the highest CH4 emissions. These emissions were influenced by nitrogen loading in area A and redox potential in area C, as well as shifts in microbial communities and functional gene abundance. Key methanogens, including Methanomicrobiales, Candidatus Methanofastidiosum and Methylthiophilus may play an important role in CH4 production. Furthermore, in comparison to the lake center, CH4 fluxes from the lake center were typically higher than those from the lake ATTZ during autumn and summer (p < 0.05). Our findings confirm that the lake ATTZ characterized by significant variability in carbon emissions across different inundation zones, plays a crucial role in estimating the contributions of freshwater ecosystems to global GHGs emissions.